@michaelborck/honeyguide-core 0.6.0 → 0.7.0

package/dist/rank/reranker.js

@@ -0,0 +1,30 @@
+import { createEmbeddingProvider } from './embeddings.js';
+import { semanticScores } from './semantic.js';
+import { OllamaDecisionReranker } from './decision.js';
+/** Embedding-based re-ranking (ADR-0015). */
+export class EmbeddingReranker {
+    provider;
+    name = 'embeddings';
+    constructor(provider) {
+        this.provider = provider;
+    }
+    score(topic, candidates) {
+        return semanticScores(topic, candidates, this.provider);
+    }
+}
+/**
+ * Pick the best available local re-ranker (ADR-0015, ADR-0016). A System One
+ * decision model is preferred when configured because it judges relevance
+ * directly; embeddings are the fallback. With neither, ranking is unchanged.
+ */
+export function createReranker(config) {
+    if (config.decisionUrl) {
+        return new OllamaDecisionReranker(config.decisionUrl, config.decisionModel ?? 'tev1:0.8b', config.decisionApiKey);
+    }
+    if (config.embeddingUrl) {
+        const provider = createEmbeddingProvider(config);
+        return provider ? new EmbeddingReranker(provider) : null;
+    }
+    return null;
+}
+//# sourceMappingURL=reranker.js.map

package/dist/rank/reranker.js.map

@@ -0,0 +1 @@
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package/dist/rank/semantic.d.ts

@@ -0,0 +1,14 @@
+import type { Candidate } from '../retrieval/candidates.js';
+import type { EmbeddingProvider } from './embeddings.js';
+/** Cosine similarity of two vectors; 0 when either is empty or mismatched. */
+export declare function cosineSimilarity(a: number[], b: number[]): number;
+/** The text embedded for a candidate: enough to judge topical relevance. */
+export declare function candidateText(candidate: Candidate): string;
+/**
+ * Score each candidate against the topic by embedding similarity. Returns a
+ * map keyed by candidate object (identity), not by URL, because duplicate
+ * URLs are already deduplicated upstream.
+ */
+export declare function semanticScores(topic: string, candidates: Candidate[], provider: EmbeddingProvider): Promise<Map<Candidate, number>>;
+/** Highest score first; candidates without a score keep their relative order. */
+export declare function orderByScores(candidates: Candidate[], scores: Map<Candidate, number>): Candidate[];

package/dist/rank/semantic.js

@@ -0,0 +1,58 @@
+const MAX_TEXT_CHARS = 1200;
+/** Cosine similarity of two vectors; 0 when either is empty or mismatched. */
+export function cosineSimilarity(a, b) {
+    if (!a.length || a.length !== b.length)
+        return 0;
+    let dot = 0;
+    let normA = 0;
+    let normB = 0;
+    for (let i = 0; i < a.length; i++) {
+        dot += a[i] * b[i];
+        normA += a[i] * a[i];
+        normB += b[i] * b[i];
+    }
+    if (!normA || !normB)
+        return 0;
+    return dot / (Math.sqrt(normA) * Math.sqrt(normB));
+}
+/** The text embedded for a candidate: enough to judge topical relevance. */
+export function candidateText(candidate) {
+    return [candidate.title, candidate.venue, candidate.description]
+        .filter(Boolean)
+        .join('. ')
+        .slice(0, MAX_TEXT_CHARS);
+}
+/**
+ * Score each candidate against the topic by embedding similarity. Returns a
+ * map keyed by candidate object (identity), not by URL, because duplicate
+ * URLs are already deduplicated upstream.
+ */
+export async function semanticScores(topic, candidates, provider) {
+    const scores = new Map();
+    if (!candidates.length)
+        return scores;
+    const texts = [topic, ...candidates.map(candidateText)];
+    const vectors = await provider.embed(texts);
+    if (vectors.length !== texts.length) {
+        throw new Error('embedding count did not match the request');
+    }
+    const [topicVector, ...candidateVectors] = vectors;
+    candidates.forEach((candidate, i) => {
+        scores.set(candidate, cosineSimilarity(topicVector, candidateVectors[i]));
+    });
+    return scores;
+}
+/** Highest score first; candidates without a score keep their relative order. */
+export function orderByScores(candidates, scores) {
+    return candidates
+        .map((candidate, index) => ({ candidate, index, score: scores.get(candidate) }))
+        .sort((a, b) => {
+        const sa = a.score ?? Number.NEGATIVE_INFINITY;
+        const sb = b.score ?? Number.NEGATIVE_INFINITY;
+        if (sa !== sb)
+            return sb - sa;
+        return a.index - b.index;
+    })
+        .map((entry) => entry.candidate);
+}
+//# sourceMappingURL=semantic.js.map

package/dist/rank/semantic.js.map

@@ -0,0 +1 @@
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package/dist/retrieval/arxiv.d.ts

@@ -0,0 +1,24 @@
+import type { Candidate } from './candidates.js';
+export interface ArxivEntry {
+    title: string;
+    authors: string[];
+    year: number | null;
+    /** Canonical abs URL, without a version suffix. */
+    url: string;
+    summary?: string;
+}
+/**
+ * arXiv preprint discovery (ADR-0013). Preprints are a structural blind spot
+ * for Crossref/OpenAlex discovery, and the Atom API is keyless and
+ * authoritative for its own corpus.
+ */
+export declare function searchArxiv(topic: string): Promise<Candidate[]>;
+/**
+ * arXiv treats a bare multi-word phrase as an impossible exact match, so
+ * build a phrase query from the topic's content phrases and OR them, the same
+ * way OpenAlex and Open Library are queried.
+ */
+export declare function buildArxivQuery(topic: string): string;
+/** Parse the flat, machine-generated Atom feed without an XML dependency. */
+export declare function parseArxivFeed(xml: string): ArxivEntry[];
+export declare function arxivEntriesToCandidates(entries: ArxivEntry[]): Candidate[];

package/dist/retrieval/arxiv.js

@@ -0,0 +1,94 @@
+import { extractPhrases } from './query.js';
+import { throttle } from './rateLimit.js';
+const ENDPOINT = 'https://export.arxiv.org/api/query';
+const API_TIMEOUT_MS = 10_000;
+const SERVICE = 'arxiv';
+// arXiv's terms of use ask for at most one request every three seconds.
+const MIN_INTERVAL_MS = 3100;
+/**
+ * arXiv preprint discovery (ADR-0013). Preprints are a structural blind spot
+ * for Crossref/OpenAlex discovery, and the Atom API is keyless and
+ * authoritative for its own corpus.
+ */
+export async function searchArxiv(topic) {
+    await throttle(SERVICE, MIN_INTERVAL_MS);
+    const searchQuery = buildArxivQuery(topic);
+    if (!searchQuery)
+        return [];
+    const params = new URLSearchParams({
+        search_query: searchQuery,
+        start: '0',
+        max_results: '8',
+    });
+    const res = await fetch(`${ENDPOINT}?${params}`, {
+        headers: { accept: 'application/atom+xml', 'user-agent': 'Honeyguide/1.0' },
+        signal: AbortSignal.timeout(API_TIMEOUT_MS),
+    });
+    if (!res.ok)
+        throw new Error(`HTTP ${res.status} from arxiv.org`);
+    return arxivEntriesToCandidates(parseArxivFeed(await res.text()));
+}
+/**
+ * arXiv treats a bare multi-word phrase as an impossible exact match, so
+ * build a phrase query from the topic's content phrases and OR them, the same
+ * way OpenAlex and Open Library are queried.
+ */
+export function buildArxivQuery(topic) {
+    const phrases = extractPhrases(topic, 3);
+    if (phrases.length) {
+        return phrases.map((p) => `all:"${p}"`).join(' OR ');
+    }
+    const fallback = topic.replace(/["\\]/g, ' ').replace(/\s+/g, ' ').trim();
+    return fallback ? `all:${fallback}` : '';
+}
+/** Parse the flat, machine-generated Atom feed without an XML dependency. */
+export function parseArxivFeed(xml) {
+    const entries = [];
+    for (const match of xml.matchAll(/<entry>([\s\S]*?)<\/entry>/g)) {
+        const block = match[1];
+        const title = block.match(/<title>([\s\S]*?)<\/title>/)?.[1];
+        if (!title)
+            continue;
+        const id = block.match(/<id>https?:\/\/arxiv\.org\/abs\/([^<]+)<\/id>/)?.[1];
+        if (!id)
+            continue;
+        const published = block.match(/<published>(\d{4})-/)?.[1];
+        const summary = block.match(/<summary>([\s\S]*?)<\/summary>/)?.[1];
+        entries.push({
+            title: clean(decodeXmlEntities(title)),
+            authors: [...block.matchAll(/<name>([\s\S]*?)<\/name>/g)]
+                .map((a) => clean(decodeXmlEntities(a[1])))
+                .filter(Boolean),
+            year: published ? Number(published) : null,
+            url: `https://arxiv.org/abs/${id.replace(/v\d+$/, '')}`,
+            summary: summary ? clean(decodeXmlEntities(summary)) : undefined,
+        });
+    }
+    return entries;
+}
+export function arxivEntriesToCandidates(entries) {
+    return entries.map((entry) => ({
+        title: entry.title,
+        url: entry.url,
+        format: 'paper',
+        authors: entry.authors,
+        year: entry.year,
+        description: entry.summary ? entry.summary.slice(0, 600) : undefined,
+        // arXiv preprints are freely readable by definition.
+        licensing: 'link-only',
+        origin: 'arxiv',
+        databaseAttested: true,
+    }));
+}
+function decodeXmlEntities(s) {
+    return s
+        .replace(/&lt;/g, '<')
+        .replace(/&gt;/g, '>')
+        .replace(/&quot;/g, '"')
+        .replace(/&#39;/g, "'")
+        .replace(/&amp;/g, '&');
+}
+function clean(s) {
+    return s.replace(/\s+/g, ' ').trim();
+}
+//# sourceMappingURL=arxiv.js.map

package/dist/retrieval/arxiv.js.map

@@ -0,0 +1 @@
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package/dist/retrieval/breaker.d.ts

@@ -0,0 +1,16 @@
+/**
+ * Per-host circuit breaker. After a few consecutive failures a host is
+ * skipped for a cooldown, so one dead API does not add latency to every
+ * request. The first success closes the circuit again.
+ */
+export declare class CircuitBreaker {
+    private readonly threshold;
+    private readonly cooldownMs;
+    private readonly failures;
+    constructor(threshold?: number, cooldownMs?: number);
+    canRequest(host: string, now?: number): boolean;
+    recordFailure(host: string, now?: number): void;
+    recordSuccess(host: string): void;
+    reset(): void;
+}
+export declare const defaultBreaker: CircuitBreaker;

package/dist/retrieval/breaker.js

@@ -0,0 +1,42 @@
+/**
+ * Per-host circuit breaker. After a few consecutive failures a host is
+ * skipped for a cooldown, so one dead API does not add latency to every
+ * request. The first success closes the circuit again.
+ */
+export class CircuitBreaker {
+    threshold;
+    cooldownMs;
+    failures = new Map();
+    constructor(threshold = 3, cooldownMs = 60_000) {
+        this.threshold = threshold;
+        this.cooldownMs = cooldownMs;
+    }
+    canRequest(host, now = Date.now()) {
+        const state = this.failures.get(host);
+        if (!state)
+            return true;
+        if (state.until > now)
+            return false;
+        // Only an expired *open* circuit resets the count; a closed circuit keeps
+        // accumulating consecutive failures.
+        if (state.until > 0)
+            this.failures.delete(host);
+        return true;
+    }
+    recordFailure(host, now = Date.now()) {
+        const state = this.failures.get(host);
+        const count = (state?.count ?? 0) + 1;
+        this.failures.set(host, {
+            count,
+            until: count >= this.threshold ? now + this.cooldownMs : 0,
+        });
+    }
+    recordSuccess(host) {
+        this.failures.delete(host);
+    }
+    reset() {
+        this.failures.clear();
+    }
+}
+export const defaultBreaker = new CircuitBreaker();
+//# sourceMappingURL=breaker.js.map

package/dist/retrieval/breaker.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"breaker.js","sourceRoot":"","sources":["../../src/retrieval/breaker.ts"],"names":[],"mappings":"AAMA;;;;GAIG;AACH,MAAM,OAAO,cAAc;IAIN;IACA;IAJF,QAAQ,GAAG,IAAI,GAAG,EAAwB,CAAC;IAE5D,YACmB,YAAY,CAAC,EACb,aAAa,MAAM;QADnB,cAAS,GAAT,SAAS,CAAI;QACb,eAAU,GAAV,UAAU,CAAS;IACnC,CAAC;IAEJ,UAAU,CAAC,IAAY,EAAE,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE;QACvC,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACtC,IAAI,CAAC,KAAK;YAAE,OAAO,IAAI,CAAC;QACxB,IAAI,KAAK,CAAC,KAAK,GAAG,GAAG;YAAE,OAAO,KAAK,CAAC;QACpC,0EAA0E;QAC1E,qCAAqC;QACrC,IAAI,KAAK,CAAC,KAAK,GAAG,CAAC;YAAE,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QAChD,OAAO,IAAI,CAAC;IACd,CAAC;IAED,aAAa,CAAC,IAAY,EAAE,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE;QAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACtC,MAAM,KAAK,GAAG,CAAC,KAAK,EAAE,KAAK,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC;QACtC,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,EAAE;YACtB,KAAK;YACL,KAAK,EAAE,KAAK,IAAI,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC;SAC3D,CAAC,CAAC;IACL,CAAC;IAED,aAAa,CAAC,IAAY;QACxB,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;IAC7B,CAAC;IAED,KAAK;QACH,IAAI,CAAC,QAAQ,CAAC,KAAK,EAAE,CAAC;IACxB,CAAC;CACF;AAED,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,cAAc,EAAE,CAAC"}

package/dist/retrieval/cache.d.ts

@@ -0,0 +1,8 @@
+/**
+ * Small process-local JSON cache for retrieval APIs. Repeated topics and
+ * batch runs then cost nothing, and the upstream APIs see fewer requests.
+ * Keyed by full URL, so headers and query strings are part of the identity.
+ */
+export declare function getCachedJson<T>(key: string, now?: number, ttlMs?: number): T | undefined;
+export declare function setCachedJson(key: string, value: unknown, now?: number): void;
+export declare function clearJsonCache(): void;

package/dist/retrieval/cache.js

@@ -0,0 +1,33 @@
+const cache = new Map();
+const DEFAULT_TTL_MS = 10 * 60 * 1000;
+const MAX_ENTRIES = 500;
+/**
+ * Small process-local JSON cache for retrieval APIs. Repeated topics and
+ * batch runs then cost nothing, and the upstream APIs see fewer requests.
+ * Keyed by full URL, so headers and query strings are part of the identity.
+ */
+export function getCachedJson(key, now = Date.now(), ttlMs = DEFAULT_TTL_MS) {
+    const entry = cache.get(key);
+    if (!entry)
+        return undefined;
+    if (now - entry.at > ttlMs) {
+        cache.delete(key);
+        return undefined;
+    }
+    // Refresh insertion order so the eviction below is least-recently-used.
+    cache.delete(key);
+    cache.set(key, entry);
+    return entry.value;
+}
+export function setCachedJson(key, value, now = Date.now()) {
+    if (cache.size >= MAX_ENTRIES) {
+        const oldest = cache.keys().next().value;
+        if (oldest !== undefined)
+            cache.delete(oldest);
+    }
+    cache.set(key, { value, at: now });
+}
+export function clearJsonCache() {
+    cache.clear();
+}
+//# sourceMappingURL=cache.js.map

package/dist/retrieval/cache.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"cache.js","sourceRoot":"","sources":["../../src/retrieval/cache.ts"],"names":[],"mappings":"AAKA,MAAM,KAAK,GAAG,IAAI,GAAG,EAAsB,CAAC;AAC5C,MAAM,cAAc,GAAG,EAAE,GAAG,EAAE,GAAG,IAAI,CAAC;AACtC,MAAM,WAAW,GAAG,GAAG,CAAC;AAExB;;;;GAIG;AACH,MAAM,UAAU,aAAa,CAC3B,GAAW,EACX,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,EAChB,KAAK,GAAG,cAAc;IAEtB,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;IAC7B,IAAI,CAAC,KAAK;QAAE,OAAO,SAAS,CAAC;IAC7B,IAAI,GAAG,GAAG,KAAK,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC;QAC3B,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QAClB,OAAO,SAAS,CAAC;IACnB,CAAC;IACD,wEAAwE;IACxE,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;IAClB,KAAK,CAAC,GAAG,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC;IACtB,OAAO,KAAK,CAAC,KAAU,CAAC;AAC1B,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,GAAW,EAAE,KAAc,EAAE,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE;IACzE,IAAI,KAAK,CAAC,IAAI,IAAI,WAAW,EAAE,CAAC;QAC9B,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,EAAE,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC;QACzC,IAAI,MAAM,KAAK,SAAS;YAAE,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IACjD,CAAC;IACD,KAAK,CAAC,GAAG,CAAC,GAAG,EAAE,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC;AACrC,CAAC;AAED,MAAM,UAAU,cAAc;IAC5B,KAAK,CAAC,KAAK,EAAE,CAAC;AAChB,CAAC"}

package/dist/retrieval/candidates.d.ts

@@ -16,7 +16,7 @@ export interface Candidate {
     description?: string;
     thumbnailUrl?: string;
     /** Where this candidate came from, for provenance and source-typing. */
-    origin: 'openalex' | 'crossref' | 'itunes' | 'openlibrary' | 'youtube' | 'searxng';
+    origin: 'openalex' | 'crossref' | 'semantic-scholar' | 'europepmc' | 'arxiv' | 'itunes' | 'openlibrary' | 'youtube' | 'searxng' | 'brave' | 'serper';
     /** True when the origin is an academic database, so existence is already attested. */
     databaseAttested: boolean;
 }

package/dist/retrieval/candidates.js

@@ -1,11 +1,35 @@
+import { getCachedJson, setCachedJson } from './cache.js';
+import { defaultBreaker } from './breaker.js';
 const FETCH_TIMEOUT_MS = 8000;
 export async function fetchJson(url, headers = {}) {
-    const res = await fetch(url, {
-        headers: { accept: 'application/json', ...headers },
-        signal: AbortSignal.timeout(FETCH_TIMEOUT_MS),
-    });
-    if (!res.ok)
-        throw new Error(`HTTP ${res.status} from ${new URL(url).host}`);
-    return res.json();
+    const cached = getCachedJson(url);
+    if (cached !== undefined)
+        return cached;
+    let host = 'unknown';
+    try {
+        host = new URL(url).host;
+    }
+    catch {
+        // Let fetch() report the malformed URL below.
+    }
+    if (!defaultBreaker.canRequest(host)) {
+        throw new Error(`Skipping ${host}: recent failures (circuit open)`);
+    }
+    try {
+        const res = await fetch(url, {
+            headers: { accept: 'application/json', ...headers },
+            signal: AbortSignal.timeout(FETCH_TIMEOUT_MS),
+        });
+        if (!res.ok)
+            throw new Error(`HTTP ${res.status} from ${host}`);
+        const data = await res.json();
+        setCachedJson(url, data);
+        defaultBreaker.recordSuccess(host);
+        return data;
+    }
+    catch (error) {
+        defaultBreaker.recordFailure(host);
+        throw error;
+    }
 }
 //# sourceMappingURL=candidates.js.map

package/dist/retrieval/candidates.js.map

@@ -1 +1 @@
-{"version":3,"file":"candidates.js","sourceRoot":"","sources":["../../src/retrieval/candidates.ts"],"names":[],"mappings":"AAwBA,MAAM,gBAAgB,GAAG,IAAI,CAAC;AAE9B,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,GAAW,EAAE,UAAkC,EAAE;IAC/E,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;QAC3B,OAAO,EAAE,EAAE,MAAM,EAAE,kBAAkB,EAAE,GAAG,OAAO,EAAE;QACnD,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,gBAAgB,CAAC;KAC9C,CAAC,CAAC;IACH,IAAI,CAAC,GAAG,CAAC,EAAE;QAAE,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,SAAS,IAAI,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;IAC7E,OAAO,GAAG,CAAC,IAAI,EAAE,CAAC;AACpB,CAAC"}
+{"version":3,"file":"candidates.js","sourceRoot":"","sources":["../../src/retrieval/candidates.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAE,aAAa,EAAE,MAAM,YAAY,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,cAAc,CAAC;AAmC9C,MAAM,gBAAgB,GAAG,IAAI,CAAC;AAE9B,MAAM,CAAC,KAAK,UAAU,SAAS,CAAC,GAAW,EAAE,UAAkC,EAAE;IAC/E,MAAM,MAAM,GAAG,aAAa,CAAU,GAAG,CAAC,CAAC;IAC3C,IAAI,MAAM,KAAK,SAAS;QAAE,OAAO,MAAM,CAAC;IAExC,IAAI,IAAI,GAAG,SAAS,CAAC;IACrB,IAAI,CAAC;QACH,IAAI,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC;IAC3B,CAAC;IAAC,MAAM,CAAC;QACP,8CAA8C;IAChD,CAAC;IACD,IAAI,CAAC,cAAc,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;QACrC,MAAM,IAAI,KAAK,CAAC,YAAY,IAAI,kCAAkC,CAAC,CAAC;IACtE,CAAC;IAED,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;YAC3B,OAAO,EAAE,EAAE,MAAM,EAAE,kBAAkB,EAAE,GAAG,OAAO,EAAE;YACnD,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,gBAAgB,CAAC;SAC9C,CAAC,CAAC;QACH,IAAI,CAAC,GAAG,CAAC,EAAE;YAAE,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,SAAS,IAAI,EAAE,CAAC,CAAC;QAChE,MAAM,IAAI,GAAG,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC;QAC9B,aAAa,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;QACzB,cAAc,CAAC,aAAa,CAAC,IAAI,CAAC,CAAC;QACnC,OAAO,IAAI,CAAC;IACd,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,cAAc,CAAC,aAAa,CAAC,IAAI,CAAC,CAAC;QACnC,MAAM,KAAK,CAAC;IACd,CAAC;AACH,CAAC"}

package/dist/retrieval/counterpoint.js

@@ -38,6 +38,7 @@ async function llmCounterQueries(topic, config) {
                 `credible material which DISAGREES with, criticises, or complicates ` +
                 `this topic's usual framing. One query per line, queries only.`,
             stream: false,
+            think: false,
             options: { num_predict: 60, temperature: 0.4 },
         }),
         signal: AbortSignal.timeout(QUERY_TIMEOUT_MS),

package/dist/retrieval/counterpoint.js.map

@@ -1 +1 @@
-{"version":3,"file":"counterpoint.js","sourceRoot":"","sources":["../../src/retrieval/counterpoint.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAE5C,MAAM,gBAAgB,GAAG,MAAM,CAAC;AAEhC;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,oBAAoB,CACxC,KAAa,EACb,MAAsB;IAEtB,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;QACrB,IAAI,CAAC;YACH,MAAM,OAAO,GAAG,MAAM,iBAAiB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;YACvD,IAAI,OAAO,CAAC,MAAM;gBAAE,OAAO,OAAO,CAAC;QACrC,CAAC;QAAC,MAAM,CAAC;YACP,gCAAgC;QAClC,CAAC;IACH,CAAC;IACD,OAAO,uBAAuB,CAAC,KAAK,CAAC,CAAC;AACxC,CAAC;AAED,MAAM,UAAU,uBAAuB,CAAC,KAAa;IACnD,MAAM,OAAO,GAAG,cAAc,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC;IACzC,MAAM,QAAQ,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;IACjE,OAAO,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,YAAY,EAAE,GAAG,CAAC,uBAAuB,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;AAC9F,CAAC;AAED,KAAK,UAAU,iBAAiB,CAAC,KAAa,EAAE,MAAsB;IACpE,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,MAAM,CAAC,SAAU,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,eAAe,EAAE;QAC9E,MAAM,EAAE,MAAM;QACd,OAAO,EAAE;YACP,cAAc,EAAE,kBAAkB;YAClC,GAAG,CAAC,MAAM,CAAC,YAAY,CAAC,CAAC,CAAC,EAAE,aAAa,EAAE,UAAU,MAAM,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SACnF;QACD,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;YACnB,KAAK,EAAE,MAAM,CAAC,WAAW,IAAI,aAAa;YAC1C,MAAM,EACJ,4BAA4B,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,OAAO;gBACvD,gEAAgE;gBAChE,qEAAqE;gBACrE,+DAA+D;YACjE,MAAM,EAAE,KAAK;YACb,OAAO,EAAE,EAAE,WAAW,EAAE,EAAE,EAAE,WAAW,EAAE,GAAG,EAAE;SAC/C,CAAC;QACF,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,gBAAgB,CAAC;KAC9C,CAAC,CAAC;IACH,IAAI,CAAC,GAAG,CAAC,EAAE;QAAE,MAAM,IAAI,KAAK,CAAC,eAAe,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;IAC1D,MAAM,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAA0B,CAAC;IACzD,OAAO,CAAC,IAAI,CAAC,QAAQ,IAAI,EAAE,CAAC;SACzB,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,uBAAuB,EAAE,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;SAC/D,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,IAAI,IAAI,CAAC,MAAM,GAAG,EAAE,CAAC;SACrD,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;AACjB,CAAC"}
+{"version":3,"file":"counterpoint.js","sourceRoot":"","sources":["../../src/retrieval/counterpoint.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAE5C,MAAM,gBAAgB,GAAG,MAAM,CAAC;AAEhC;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,oBAAoB,CACxC,KAAa,EACb,MAAsB;IAEtB,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;QACrB,IAAI,CAAC;YACH,MAAM,OAAO,GAAG,MAAM,iBAAiB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;YACvD,IAAI,OAAO,CAAC,MAAM;gBAAE,OAAO,OAAO,CAAC;QACrC,CAAC;QAAC,MAAM,CAAC;YACP,gCAAgC;QAClC,CAAC;IACH,CAAC;IACD,OAAO,uBAAuB,CAAC,KAAK,CAAC,CAAC;AACxC,CAAC;AAED,MAAM,UAAU,uBAAuB,CAAC,KAAa;IACnD,MAAM,OAAO,GAAG,cAAc,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC;IACzC,MAAM,QAAQ,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;IACjE,OAAO,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,YAAY,EAAE,GAAG,CAAC,uBAAuB,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;AAC9F,CAAC;AAED,KAAK,UAAU,iBAAiB,CAAC,KAAa,EAAE,MAAsB;IACpE,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,MAAM,CAAC,SAAU,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,eAAe,EAAE;QAC9E,MAAM,EAAE,MAAM;QACd,OAAO,EAAE;YACP,cAAc,EAAE,kBAAkB;YAClC,GAAG,CAAC,MAAM,CAAC,YAAY,CAAC,CAAC,CAAC,EAAE,aAAa,EAAE,UAAU,MAAM,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SACnF;QACD,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;YACnB,KAAK,EAAE,MAAM,CAAC,WAAW,IAAI,aAAa;YAC1C,MAAM,EACJ,4BAA4B,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,OAAO;gBACvD,gEAAgE;gBAChE,qEAAqE;gBACrE,+DAA+D;YACjE,MAAM,EAAE,KAAK;YACb,KAAK,EAAE,KAAK;YACZ,OAAO,EAAE,EAAE,WAAW,EAAE,EAAE,EAAE,WAAW,EAAE,GAAG,EAAE;SAC/C,CAAC;QACF,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,gBAAgB,CAAC;KAC9C,CAAC,CAAC;IACH,IAAI,CAAC,GAAG,CAAC,EAAE;QAAE,MAAM,IAAI,KAAK,CAAC,eAAe,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;IAC1D,MAAM,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAA0B,CAAC;IACzD,OAAO,CAAC,IAAI,CAAC,QAAQ,IAAI,EAAE,CAAC;SACzB,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,uBAAuB,EAAE,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;SAC/D,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,IAAI,IAAI,CAAC,MAAM,GAAG,EAAE,CAAC;SACrD,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;AACjB,CAAC"}

package/dist/retrieval/europePmc.d.ts

@@ -0,0 +1,32 @@
+import { type Candidate } from './candidates.js';
+interface EpmcAuthor {
+    fullName?: string;
+    lastName?: string;
+    firstName?: string;
+    collectiveName?: string;
+}
+interface EpmcResult {
+    id?: string;
+    source?: string;
+    title?: string;
+    doi?: string;
+    pubYear?: string;
+    authorList?: {
+        author?: EpmcAuthor[];
+    };
+    journalInfo?: {
+        journal?: {
+            title?: string;
+        };
+    };
+    abstractText?: string;
+    isOpenAccess?: string;
+}
+/**
+ * Europe PMC (ADR-0013): strong biomedical coverage and keyless. Used as a
+ * discovery source, not just a verification lookup, so the query is the topic
+ * rather than an exact title.
+ */
+export declare function searchEuropePmc(topic: string): Promise<Candidate[]>;
+export declare function parseEuropePmcResults(results: EpmcResult[]): Candidate[];
+export {};

package/dist/retrieval/europePmc.js

@@ -0,0 +1,62 @@
+import { fetchJson } from './candidates.js';
+import { normalizeDoi } from './paperMerge.js';
+import { throttle } from './rateLimit.js';
+const ENDPOINT = 'https://www.ebi.ac.uk/europepmc/webservices/rest/search';
+const SERVICE = 'europepmc';
+const MIN_INTERVAL_MS = 1000;
+/**
+ * Europe PMC (ADR-0013): strong biomedical coverage and keyless. Used as a
+ * discovery source, not just a verification lookup, so the query is the topic
+ * rather than an exact title.
+ */
+export async function searchEuropePmc(topic) {
+    await throttle(SERVICE, MIN_INTERVAL_MS);
+    const params = new URLSearchParams({
+        query: topic,
+        format: 'json',
+        resultType: 'core',
+        pageSize: '8',
+    });
+    const data = (await fetchJson(`${ENDPOINT}?${params}`, {
+        'user-agent': 'Honeyguide/1.0',
+    }));
+    return parseEuropePmcResults(data.resultList?.result ?? []);
+}
+export function parseEuropePmcResults(results) {
+    return results.flatMap((r) => {
+        const title = clean(r.title);
+        if (!title)
+            return [];
+        const doi = normalizeDoi(r.doi);
+        const url = (doi ? `https://doi.org/${doi}` : undefined) ??
+            (r.id && r.source
+                ? `https://europepmc.org/article/${encodeURIComponent(r.source)}/${encodeURIComponent(r.id)}`
+                : undefined);
+        if (!url)
+            return [];
+        return [
+            {
+                title,
+                url,
+                format: 'paper',
+                authors: (r.authorList?.author ?? [])
+                    .map((a) => a.collectiveName ||
+                    [a.lastName, a.firstName].filter(Boolean).join(', ') ||
+                    a.fullName ||
+                    '')
+                    .filter(Boolean),
+                year: /^\d{4}$/.test(r.pubYear ?? '') ? Number(r.pubYear) : null,
+                doi,
+                description: r.abstractText ? clean(r.abstractText).slice(0, 600) : undefined,
+                venue: r.journalInfo?.journal?.title,
+                ...(r.isOpenAccess === 'Y' ? { licensing: 'link-only' } : {}),
+                origin: 'europepmc',
+                databaseAttested: true,
+            },
+        ];
+    });
+}
+function clean(s) {
+    return (s ?? '').replace(/<[^>]+>/g, ' ').replace(/\s+/g, ' ').trim();
+}
+//# sourceMappingURL=europePmc.js.map

package/dist/retrieval/europePmc.js.map

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package/dist/retrieval/paperMerge.d.ts

@@ -0,0 +1,16 @@
+import type { Candidate } from './candidates.js';
+/**
+ * Canonical DOI form for matching: no resolver prefix, no `doi:` label,
+ * lower-case. Everything downstream compares on this.
+ */
+export declare function normalizeDoi(doi?: string | null): string | undefined;
+/** Title key for matching when a DOI is unavailable. */
+export declare function normalizeTitle(title: string): string;
+/**
+ * Merge paper candidates from several databases (ADR-0013). Duplicates are
+ * matched by normalised DOI first, then by normalised title, so a DOI-less
+ * arXiv record and a Crossref record for the same paper collapse into one.
+ * The first occurrence wins for conflicting fields; missing fields are filled
+ * from later duplicates.
+ */
+export declare function mergePaperCandidates(lists: Candidate[][]): Candidate[];